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During an expedition into fluidic space in 2409 led by Rear AdmiralTuvok, the original Dr. Cooper was assigned to the USS Venture. The Venture came under attack by first the Borg, then the Undine, and was destroyed. Cooper was replaced by an Undine who took his place in an escape pod and presumed killed, and the fake Cooper was collected by the other ships in the expedition. (STOmission: "Fluid Dynamics")

The rationale for placing the original Cooper's replacement at this point is a line by Cooper when his escape pod is picked up by the player character. He states that the Undine attackers "were so strong, and we were so weak", in clear reference to the Undine war cry "The weak will perish!"

In 2410 the Cooper Undine mentally attacked Tuvok during the Undine invasion of the Solsystem. Tuvok was able to turn the tables and discovered that the Sol attack was a diversion and the true target was Qo'noS. (STOmission: "Surface Tension")

The Cooper Undine mentally attacked Tuvok again in the Delta Quadrant, but Tuvok and another captain fought him off in a mind meld and confronted him aboard his command bioship. Tuvok convinced the ship, which was fully sapient, that by working together the "strong" survive. Cooper tried to deflect this but the bioship thought otherwise and destroyed him. (STOmission: "Mindscape")